Scarlets made a pre-tax loss of more than £1.7m in the latest available accounts for the year ending June 2014.
Fellow Welsh rugby region Cardiff Blues recorded a loss of almost £240,000.
Scarlets' loss was £1m more than the previous year, a sum blamed partly on the two-year dispute with the Welsh Rugby Union that ended in a £60m Rugby Services Agreement in August 2014.
Chairman Nigel Short, in his statement, said Scarlets had been "materially at risk" due to the agreement's delay.
The four Welsh regions, which also include Ospreys and Newport Gwent Dragons, had been in dispute with the WRU over areas of concern including levels of funding and proposed new competitions.
Negotiations between the two sides had been fraught and lengthy, with Scarlets noting in the strategic report section of the accounts that legal costs had also risen sharply.
"Included in the... loss is a number of abnormal and non-recurring costs," read the statement.
"The long and protracted negotiations with the WRU not only had a significant and negative impact on our financial performance but also directly cost in the region of £200,000 in legal and professional fees necessary to reach a satisfactory conclusion."
Creditors include £2.6m owed to Carmarthenshire County Council, with interest paid at 7% per annum, and due for repayment in 2023.
The Llanelli-based region also says it "invested an additional £500,000 directly into our rugby playing budget and backroom coaching group".
Scarlets qualified for the 2014-15 European Champions Cup and again secured a place in the top-tier competition next season after finishing sixth in the Pro12 league.
Blues' loss was better than the previous year, with the £238,552 in the red an improvement on the £259,450 from 2013.
The region's main creditor is Peter Thomas with a non-interest loan of £6.12m owed to him, plus a further interest-bearing loan of £1.9m owed to Atlantic Properties Developments PLC - a company under the control of Thomas.
The region increased its turnover by 6%, helped by a return to its traditional Cardiff Arms Park home, new sponsorship and a reduction in the wage bill.
In his statement, Blues chairman Richard Holland also noted the difficulties the region had faced during the dispute with the WRU.
"It placed enormous pressure on the business and restricted our ability to plan with any certainty for the future," Holland wrote.
"However, through strong and successful management we have ensured we have continued to make strides forward and record another improving financial performance."
A 10th-place finish in the Pro12 saw Blues finish lowest of the Welsh regions and miss out on a place in the Champions Cup, instead having to settle for the Challenge Cup for a second season.
Blues did reach the quarter-finals of the second-tier European competition last season, where they were beaten by Dragons.